First representative complete mitochondrial genome of the Taphozous melanopogon Temminck, 1841 (Chiroptera: Emballonuridae) from China

Abstract In this study, we present the first representative complete Taphozous melanopogon mitochondrial genome from China. Its mitochondrial genome was assembled and annotated using MitoZ. The genome is a circular molecule of 16,566 bp in length, including 22 transfer RNA genes, 2 ribosomal RNA genes, 13 protein-coding genes, and a control region. Although maximum-likelihood and Bayesian inference phylogenetic trees indicate that the super family Emballonuridea forms a sister taxon with Noctilionidea instead of Vespertilionidea, mitochondrial genes provide only part of the phylogenetic information, and phylogenetic inferences utilizing nuclear genes are needed in future toward resolving phylogenetic relationship among Vespertilionidea, Noctilionidea, and Emballonuridea.

In this study, a male individual of Taphozous melanopogon (Voucher No. GZHU 15063) was sampled in a cave near Longmen Town, Guangdong Province, China (23.59 N,114.29 E) in 2015. The person in charge of the collection: Yi Wu (email: wuyizhouq@263.net). The specimen is presently deposited at Key Laboratory of Conservation and Application in Biodiversity of South China, School of Life Sciences, Guangzhou University (contact email: wuyizhouq@263.net). Permission for field surveys and sampling was granted by the Forestry Administration of Guangdong Province, China. The identification of Taphozous melanopogon was confirmed by phylogenetic analyses using datasets comprising cytb and cox1 as well as morphological examinations (Corbet and Hill 1992;Dengis 1996;Colket and Wilson 1998;Bates et al. 2000). Total genome was extracted from liver tissue using MiniBEST Universal Genomic DNA Extraction kit (TAKARA, Dalian) and was further sequenced paired-end using MGISEQ-2000 sequencing platforms, following a PE150 protocol. Based upon 5GB data a complete mitochondrial genome was assembled and annotated via MitoZ v2.4 which is specialized for mitochondrial genome (Meng et al. 2019).
Our study represents the first mitochondrial report of genus Taphozous. Mitochondrial genome of the Taphozous melanopogon is 16,566 bp in length (Genbank accession No. MZ286363), containing 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a control region. Among the 13 protein-coding genes, atp8 and atp6 were overlapped by 43 bp, nad4L and nad4 were overlapped by 7 bp. Most start codon of the protein-coding genes is ATG, except for nad2(ATT) and nad3 (ATT), nad5 (ATA). Termination codon of eight protein-coding genes were TAA (atp8, atp6, cox1, cox2, nad1, nad4L, nad5, and nad6), while the rest genes were different, including, nad2 (TAG), nad3(TAG). Three genes end with an incomplete stop codon TA-(cox3) and T-(cytb, nad4), which can be modified by the polyadenylation after transcript processing (Ojala et al. 1981). rrnS gene and rrnL were separated by trnV, lengths of them were 970 bp and 1561 bp, respectively. Control region is between the trnF and the trnP, and it is 1138 bp in length.
In phylogenetic analyses, we covered the sequence of representatives from Emballonuridea, Noctilionidea, Vespertilionidea, Rhinolophoidea, and Pteropodidae. Yangochiroptera lineages (Rhinolophoidea and Pteropodidae) were set as outgroup (Figure 1). The 37 genes were extracted for phylogenetic inference using by PhyloSuite v1.1.2 (Zhang et al. 2020). While the mitochondrial control region was eliminated because of its high variability. We aligned our sequence matrixes using MUSCLE (Edgar 2004) and optimized the alignments of protein-coding genes using MACSE v2 (Ranwez et al. 2018). Conserved blocks were further identified of using Gblock (Talavera and Castresana 2007). ModelFinder was adopted to determinate optimal model for each gene partition (Kalyaanamoorthy et al. 2017). The maximum-likelihood phylogenetic trees were inferred using IQ-Tree v2.0.3 with 1000 bootstraps setting (Minh et al. 2020), Bayesian phylogenetic inference was using MrBayes v3.2.6. Monte Carlo-Monte Carlo chains were simultaneously run for 10 million generations, with sampling conducted every 1000 generations. The confidence values of the tree are presented as Bayesian posterior probabilities. (Ronquist et al. 2012). Both phylogenies depicted Emballonuridea as sister taxon to Noctilionidea (Figure 1). Given the fact that mitochondrial genes provide only part of the phylogenetic information. Discordance between mitochondrial genes and nuclear genes in animals (Toews and Brelsford 2012), phylogenetic inference utilizing nuclear genes are needed in future toward resolving phylogenetic relationship among Vespertilionidea, Noctilionidea and Emballonuridea.

Author contributions
Yi Wu and Wen-hua Yu designed the study; Yan-nan Li preformed phylogenetic analyses; Sanjan Thapa revised the manuscript.

Data availability statement
The data that support the findings of this study are openly available in NCBI at https://www.ncbi.nlm.nih.gov/nuccore/MZ286363, reference number MZ286363. The associated BioProject, BioSample and SRA numbers are PRJNA730371, SAMN19236524 and SRR15311579 respectively.